Remove execute bit on all files in git repo (Submitty#2182)

* commit changes

* remove execute permission bits from some files

* remove execute bit on all files in git

* Use bash/python3 for calling things directly in git

* Fix broken path

* revert change of git permissions

* permissions

.setup/INSTALL_SUBMITTY_HELPER.sh

@@ -741,7 +741,7 @@ if [ "${WORKER}" == 0 ]; then
         # pop the first argument from the list of command args
         shift
         # pass any additional command line arguments to the run test suite
-        ${SUBMITTY_INSTALL_DIR}/test_suite/integrationTests/run.py  "$@"
+        python3 ${SUBMITTY_INSTALL_DIR}/test_suite/integrationTests/run.py  "$@"
 
         echo -e "\nCompleted Autograding Test Suite\n"
     fi
@@ -806,9 +806,3 @@ else
         sudo -H -u ${HWCRON_USER} ${SUBMITTY_INSTALL_DIR}/sbin/shipper_utils/update_and_install_workers.py
     fi
 fi
-
-# set filemode to false, so that changes to file permissions in the
-# git repository will be ignored for future diffs/commits
-pushd ${SUBMITTY_REPOSITORY}
-git config --local core.filemode false
-popd > /dev/null

.setup/bin/partial_reset.py

@@ -91,7 +91,7 @@ def main():
     os.system("mkdir -p {}/courses".format(SUBMITTY_DATA_DIR))
     os.system("mkdir -p {}/instructors".format(SUBMITTY_DATA_DIR))
     os.system("ls /home | sort > {}/instructors/valid".format(SUBMITTY_DATA_DIR))
-    os.system("{}/.setup/INSTALL_SUBMITTY.sh".format(SUBMITTY_INSTALL_DIR))
+    os.system("bash {}/.setup/INSTALL_SUBMITTY.sh".format(SUBMITTY_INSTALL_DIR))
     distro = platform.linux_distribution()[0].lower()
     if os.path.isdir(os.path.join(CURRENT_PATH, "..", "..", ".vagrant")):
         os.system("rm -rf {}/logs".format(SUBMITTY_DATA_DIR))
@@ -100,7 +100,6 @@ def main():
         os.system('mkdir {}/.vagrant/{}/logs'.format(SUBMITTY_REPOSITORY, distro))
         os.system('ln -s {}/.vagrant/{}/logs {}'.format(SUBMITTY_REPOSITORY, distro, SUBMITTY_DATA_DIR))
 
-
         os.system('mkdir {}/.vagrant/{}/logs/autograding'.format(SUBMITTY_REPOSITORY, distro))
         os.system('mkdir {}/.vagrant/{}/logs/access'.format(SUBMITTY_REPOSITORY, distro))
         os.system('mkdir {}/.vagrant/{}/logs/site_errors'.format(SUBMITTY_REPOSITORY, distro))

.setup/install_system.sh

@@ -70,7 +70,7 @@ fi
 # USERS SETUP
 #################
 
-${SUBMITTY_REPOSITORY}/.setup/bin/create_untrusted_users.py
+python3 ${SUBMITTY_REPOSITORY}/.setup/bin/create_untrusted_users.py
 
 # Special users and groups needed to run Submitty
 #
@@ -467,7 +467,7 @@ echo Beginning Submitty Setup
 #If in worker mode, run configure with --worker option.
 if [ ${WORKER} == 1 ]; then
     echo  Running configure submitty in worker mode
-    ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --worker
+    python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --worker
 else
     if [ ${VAGRANT} == 1 ]; then
     # This should be set by setup_distro.sh for whatever distro we have, but
@@ -482,10 +482,10 @@ else
     ${SUBMISSION_URL}
     ${GIT_URL}/git
 
-    1" | ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --debug
+    1" | python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --debug
 
     else
-        ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py
+        python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py
     fi
 fi
 
@@ -509,7 +509,7 @@ if [ ${WORKER} == 0 ]; then
 fi
 
 echo Beginning Install Submitty Script
-source ${SUBMITTY_INSTALL_DIR}/.setup/INSTALL_SUBMITTY.sh clean
+bash ${SUBMITTY_INSTALL_DIR}/.setup/INSTALL_SUBMITTY.sh clean
 
 
 # (re)start the submitty grading scheduler daemon
@@ -570,7 +570,7 @@ if [ ${WORKER} == 0 ]; then
         chmod -R 770 ${SUBMITTY_DATA_DIR}/logs/site_errors
 
         # Call helper script that makes the courses and refreshes the database
-        ${SUBMITTY_REPOSITORY}/.setup/bin/setup_sample_courses.py --submission_url ${SUBMISSION_URL}
+        python3 ${SUBMITTY_REPOSITORY}/.setup/bin/setup_sample_courses.py --submission_url ${SUBMISSION_URL}
 
         #################################################################
         # SET CSV FIELDS (for classlist upload data)

.setup/travis/setup.sh

@@ -32,7 +32,7 @@ sudo mkdir -p ${SUBMITTY_INSTALL_DIR}
 sudo mkdir -p ${SUBMITTY_DATA_DIR}
 sudo cp -R ${TRAVIS_BUILD_DIR} ${SUBMITTY_REPOSITORY}
 
-sudo ${DIR}/../bin/create_untrusted_users.py
+sudo python3 ${DIR}/../bin/create_untrusted_users.py
 
 sudo addgroup hwcronphp
 sudo addgroup course_builders
@@ -59,7 +59,7 @@ America/New_York
 http://localhost
 http://localhost/git
 
-${AUTH_METHOD}" | sudo ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --debug
+${AUTH_METHOD}" | sudo python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --debug
 
 
 mkdir -p ${SUBMITTY_DATA_DIR}/instructors
@@ -79,4 +79,4 @@ sudo usermod -a -G travis hwphp
 # necessary to pass config path as submitty_repository is a symlink
 sudo python3 ${SUBMITTY_REPOSITORY}/migration/migrator.py -e master -e system migrate --initial
 
-sudo /usr/local/submitty/.setup/INSTALL_SUBMITTY.sh clean
+sudo bash /usr/local/submitty/.setup/INSTALL_SUBMITTY.sh clean

.setup/vagrant/setup_vagrant.sh

@@ -15,5 +15,5 @@ if [ -x "$(command -v pip3)" ]; then
     python3 ${SUBMITTY_REPOSITORY}/.setup/bin/reset_system.py
 fi
 
-sudo ${SUBMITTY_REPOSITORY}/.setup/install_system.sh --vagrant ${@}
+sudo bash ${SUBMITTY_REPOSITORY}/.setup/install_system.sh --vagrant ${@}
 

.travis.yml

@@ -159,10 +159,10 @@ jobs:
         - export DBUS_SESSION_BUS_ADDRESS=/dev/null
         - psql -U postgres -c "CREATE ROLE hsdbu WITH SUPERUSER CREATEDB CREATEROLE LOGIN PASSWORD 'hsdbu'"
         - PGPASSWORD=hsdbu psql -d postgres -h localhost -U hsdbu -c "CREATE DATABASE submitty"
-        - sudo ./.setup/travis/autograder.sh
-        - ./.setup/travis/setup.sh
-        - sudo /usr/local/submitty/GIT_CHECKOUT/Submitty/.setup/bin/setup_sample_courses.py sample
-        - sudo ./.setup/travis/setup_test_suite.sh
+        - sudo bash .setup/travis/autograder.sh
+        - bash .setup/travis/setup.sh
+        - sudo python3 /usr/local/submitty/GIT_CHECKOUT/Submitty/.setup/bin/setup_sample_courses.py sample
+        - sudo bash .setup/travis/setup_test_suite.sh
         - sudo sed -e "s?www-data?hwphp?g" --in-place /etc/apache2/envvars
         - sudo a2enmod include rewrite actions cgi alias headers
         - echo "cgi.fix_pathinfo = 1" >> ~/.phpenv/versions/$(phpenv version-name)/etc/php.ini
@@ -245,11 +245,11 @@ jobs:
         - popd
         - sudo chmod -R 555 /usr/local/lib/python*/
         - sudo chmod -R 555 /opt/python/${PY_VERSION_3}/lib/python${PY_VERSION_3:0:3}/*
-        - sudo ./.setup/travis/autograder.sh
-        - ./.setup/travis/setup.sh
-        - sudo ./.setup/travis/setup_test_suite.sh
+        - sudo bash ./.setup/travis/autograder.sh
+        - bash ./.setup/travis/setup.sh
+        - sudo bash ./.setup/travis/setup_test_suite.sh
       script:
-        - sudo /usr/local/submitty/test_suite/integrationTests/run.py
+        - sudo python3 /usr/local/submitty/test_suite/integrationTests/run.py
     - <<: *04-integration
       env: CLANG_VER="6.0.0"
       if: branch = master OR type = pull_request

Vagrantfile

@@ -13,7 +13,7 @@ GIT_PATH=/usr/local/submitty/GIT_CHECKOUT/Submitty
 DISTRO=$(lsb_release -si | tr '[:upper:]' '[:lower:]')
 VERSION=$(lsb_release -sc | tr '[:upper:]' '[:lower:]')
 mkdir -p ${GIT_PATH}/.vagrant/${DISTRO}/${VERSION}/logs
-${GIT_PATH}/.setup/vagrant/setup_vagrant.sh #{ENV['EXTRA']} 2>&1 | tee ${GIT_PATH}/.vagrant/${DISTRO}/${VERSION}/logs/vagrant.log
+bash ${GIT_PATH}/.setup/vagrant/setup_vagrant.sh #{ENV['EXTRA']} 2>&1 | tee ${GIT_PATH}/.vagrant/${DISTRO}/${VERSION}/logs/vagrant.log
 SCRIPT
 
 unless Vagrant.has_plugin?('vagrant-vbguest')
@@ -56,13 +56,15 @@ Vagrant.configure(2) do |config|
 
   config.vm.provision :shell, :inline => " sudo timedatectl set-timezone America/New_York", run: "once"
 
-  config.vm.synced_folder '.', '/usr/local/submitty/GIT_CHECKOUT/Submitty', create: true, mount_options: ["dmode=775", "fmode=774"]
-
-  optional_repos = ["AnalysisTools","Lichen","RainbowGrades","Tutorial"]
+  owner = 'root'
+  group = 'root'
+  config.vm.synced_folder '.', '/usr/local/submitty/GIT_CHECKOUT/Submitty', create: true, owner: owner, group: group
 
+  optional_repos = %w(AnalysisTools Lichen RainbowGrades Tutorial)
   for repo in optional_repos do
-    if File.directory?(File.expand_path("../"+repo))
-      config.vm.synced_folder "../"+repo,"/usr/local/submitty/GIT_CHECKOUT/"+repo, mount_options: ["dmode=775", "fmode=774"]
+    repo_path = File.expand_path("../" + repo)
+    if File.directory?(repo_path)
+      config.vm.synced_folder repo_path,"/usr/local/submitty/GIT_CHECKOUT/" + repo, owner: owner, group: group
     end
   end